NGS module

Responsible
Carla Mavian and Matia Prosperi

TIME

CONTENT

SPEAKERS

SUNDAY 4 AUGUST

14:00
to
16:00

Introduction to command line (optional)​

TBA

16:00
to
18:00

Welcome to VEME

Luiz Alcantara

18:00
to
20:00

VEME Cocktail Event

Monday 5 AUGUST

08:00
to
08:30

Registration.

8:30
to
9:30

Introduction to next generation sequencing.

R. Scheuermann

9:30
to
10:30

Introduction to computing

D. Park

10:30
to
11:00

Coffee break.

11:00
to
12:30

Nanopore sequencing: introduction and theory

S. James, M. Moir

12:30
to
14:00

Lunch.

14:00
to
15:00

Reference alignment and SNP calling: theory

C. Mavian

15:00
to
16:00

Intro to Terra and reference alignment and SNP calling

D. Park, C. Tomkins-Tinch

16:00
to
17:00

Coffee break + poster session.

Tuesday 6 AUGUST

8:30
to
9:30

Reference alignment and SNP calling using Terra

D. Park, C. Tomkins-Tinch

9:30
to
10:30

Reference alignment and SNP calling using CLI

T. Paisie, L.S. Whitmore, C. Mavian

10:30
to
11:00

Coffee break.

11:00
to
12:30

De novo assembly

H. Schmidt

12:30
to
13:30

Lunch.

13:30
to
14:30

De novo assembly practice using Terra

D. Park, C. Tomkins-Tinch

14:30
to
15:30

De novo assembly practice using CLI

T. Paisie, L.S. Whitmore, C. Mavian

15:30
to
16:00

Coffee break.

16:00
to
16:50

Free computer time.

T. Paisie, L.S. Whitmore, C. Mavian

Wednesday 7 AUGUST

8:30
to
9:30

Bulk Transcriptomics: theory

R. Scheuermann

9:30
to
10:30

Bulk Transcriptomics: practice 1

R. Scheuermann, Z. Wallace, J. Xavier, S. James, L.S. Whitmore

10:30
to
11:00

Coffee break.

11:00
to
12:30

Bulk Transcriptomics: practice 2

R. Scheuermann, Z. Wallace, J. Xavier, S. James, L.S. Whitmore

12:30
to
13:30

Lunch.

13:30
to
14:30

Single cell transcriptomics: theory

R. Scheuermann

14:30
to
15:30

Single cell transcriptomics: practice 1

R. Scheuermann, Z. Wallace, J. Xavier, S. James, L.S. Whitmore

15:30
to
16:00

Single cell transcriptomics: practice 2

R. Scheuermann, Z. Wallace, J. Xavier, S. James, L.S. Whitmore

16:00
to
17:00

Coffee break + poster session.

17:30
to
18:45

Keynote 1:

Edward Holmes

18:45
to
20:00

Keynote 2:

Marion Koopmans

Thursday 8 August

8:30
to
9:30

Metagenomics

H. Schmidt.

9:30
to
10:30

Metagenomics: Taxonomy Classification

C. Mavian, T. Paisie, D. Park, C. Tomkins-Tinch, L.S. Whitmore

10:30
to
11:00

Coffee break.

11:00
to
12:30

Genome Detective

K. Deforche, V. Fonseca, S. James

12:30
to
13:30

Lunch.

13:30
to
14:30

Nextflow​

A. Sharma

14:30
to
15:30

Nextflow

A. Sharma

15:30
to
16:00

Coffee break.

16:00
to
17:30

Free computer time

A. Sharma, T. Paisie, L.S. Whitmore

18:30
to
20:30

Course teachers dinner